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Abstract: The vast majority of chemistry and biology occurs in solution, and new label-free analytical techniques that can help resolve solution-phase complexity at the single-molecule level can provide new microscopic perspectives of unprecedented detail. Here, we use the increased light-molecule interactions in high-finesse fiber Fabry-Pérot microcavities to detect individual biomolecules as small as 1.2 kDa (10 amino acids) with signal-to-noise ratios >100, even as the molecules are freely diffusing in solution.  Our method delivers 2D intensity and temporal profiles, enabling the distinction of sub-populations in mixed samples. Strikingly, we observe a linear relationship between passage time and molecular radius, unlocking the potential to gather crucial information about diffusion and solution-phase conformation. Furthermore, mixtures of biomolecule isomers of the same molecular weight can also be resolved. Detection is based on a novel molecular velocity filtering and dynamic thermal priming mechanism leveraging both photo-thermal bistability and Pound-Drever-Hall cavity locking. This technology holds broad potential for applications in life and chemical sciences and represents a major advancement in label-free in vitro single-molecule techniques.

Methanogens are a diverse group of archaea with ancient evolutionary origins. They are found in a wide range of anoxic environments where they carry out a form of anaerobic respiration known as methanogenesis. This process reduces simple oxidized carbon compounds to generate methane as an end product. Another group of archaea related to methanogens carry out the anaerobic oxidation of methane (AOM) and are known as anaerobic methanotrophs (ANME).  Methanogens and ANME are both key components in the global carbon cycle and play a central role in controlling atmospheric methane concentrations. Consistent with their anaerobic lifestyles and ancient evolutionary origins, methanogens and ANME contain an abundance of Fe-S cluster proteins. Radical S-adenosylmethionine (SAM) enzymes are [4Fe-4S]-cluster containing enzymes that catalyze a wide variety of difficult biochemical reactions through the generation of a highly reactive 5’-deoxyadenosyl radical. Here, we discuss our recent progress towards uncovering the functions of novel radical SAM enzymes in methanogens and ANME. We identified the missing glutamate 2,3-aminomutase important for salt tolerance in marine organisms as well as characterized the first archaeal methylthiotransferase involved in tRNA modification. 

The structure of plant cell wall carbohydrates creates the strength and flexibility of the plant cell wall, which shapes plants’ overall agronomic fitness in the field. Differences in cell wall carbohydrates and associated compounds are also influential post-harvest, since carbohydrate structural characteristics can influence a material’s food processing characteristics, feed value for livestock, and biofuel production potential.

The core areas of Dr. Schendel’s research program at the ��ɫ��Ƶ are plant cell wall characterization (especially detailed structural analysis of cell wall carbohydrates) and analysis and application of phenolics and other secondary plant metabolites. Strategic collaborations have allowed us to explore applied questions such as ruminant microbe fermentation of cell wall carbohydrates. This seminar will share results from several projects, including our in-depth characterizations of the cell walls of cool-season forages and hempseeds and exploration of their seasonal and species/cultivar variation. 

Chamikara Karunasena

Graduate Student Profile

Abstract: The immense synthetic design space and material versatility have driven the exploration and development of organic semiconductors (OSC) over several decades. While many OSC designs focus on the chemistries of the molecular or polymer building blocks, a priori, multiscale control over the solid-state morphology is required for effective application of the active layer in a given technology. However, molecular assembly during solid-state formation is a complex function interconnecting the building block chemistry and the processing environment. Insufficient knowledge as to the how these aspects engage, especially at the atomistic and molecular scales, have so far limited the ability to predict OSC solid-state morphology, leaving Edisonian approaches as the stalwart methods. Therefore, through multiscale simulations combining atomistic quantum scale modeling and modern advanced sampling molecular dynamics (MD), we aim to establish first principles understanding required to synthetically regulate solid-state morphology of organic semiconductors (OSC) as a function of molecular chemistry and processing. In turn we try to understand the deceivingly simple yet complex mechanisms behind molecular aggregation and crystallization of OSC. Simultaneously, we develop semi-to-fully automated high-throughput schemes to automate the complex and labor-intensive analyses to generate data based on various crystal structures in different crystallization environments. Ultimately, we aim to bridge molecular-scale information revealed on solid-state physical organization, understood in the context of chromophore chemistry and the molecular environment, with the macro scale properties to uncover useful guidelines for rational design and morphology regulation of OSC systems.

Graduate Student Profile

Abstract: Plant-derived compounds have the potential to produce value-added compounds with a variety of applications. For example, the lignin part of the lignocellulosic biomass, produced in large quantities as waste from the paper and pulp industries, is a rich source of phenolics with potential applications in the renewable energy sector, pharmaceutical, and chemical industries. On the other hand, plant alkaloids are the primary source for developing plant-derived therapeutics. Unfortunately, the recalcitrant nature of plant cell walls, low extraction yields of small secondary metabolites, and the lack of effective analytical methods for a rapid and accurate identification of plant-based compounds and plant’s degradation products are the major limitations in plant-based valorization efforts.

In order to address some of these challenges, this dissertation focuses on utilizing different mass spectrometry-based techniques such as UHPLC-MS, GC-MS, and direct infusion high-resolution accurate orbitrap and ion trap mass spectrometry for the detection and structure elucidation of plant-based phenolics and alkaloids in order to contribute to ongoing efforts toward valorization of plant-based compounds. Mass spectrometry-based techniques are widely used in pharmaceutical and chemical industries, and have been emerged as one of the most promising analytical techniques for the analysis of plant-based compounds.

In the second chapter of this dissertation, a mass spectrometric method based on lithium cationization was developed to sequence lignin model oligomers with mixed bonding motifs, with a potential application in facilitating the structure elucidation of lignin degradation end products with β-β and β-O-4 linkages. In the third chapter, an important lignan, syringaresinol, was characterized in bourbon whiskey. The origin of syringaresinol was investigated using a model aging experiment to further our understanding of bourbon’s chemical composition. In chapter four, the development of a mild ethanosolv treatment combined with a GC-MS method enabled the detection of several different phenolic compounds in lignocellulosic biomass, which can be potentially used to rapidly compare different biomass samples for the valorization applications. Lastly, in chapter five, synthetic methods in combination with extensive mass spectrometry-based analysis were used to semi-synthesize new plant-based alkaloids with potential applications in drug discovery and development.

Overall, these studies confirm that mass spectrometry-based techniques provide a sensitive and robust analytical platform for the analysis of plant-based products.

Graduate Student Profile

Abstract: 

Site-selective modifications of target proteins using specifically designed small molecules is a powerful tool that has been extensively utilized for drug discovery. Small molecules can modify proteins either covalently or non-covalently depending on their structures and intrinsic chemical reactivity. Covalent chemical modification presents a more stable and often irreversible interaction with target proteins; unlike non-covalent binders, which form weak, reversible interactions with protein. Therefore, covalent modifiers represent an effective class of therapeutics due to their stability and irreversibility once bound to target proteins of interest. I hypothesized that tuning biocompatible, high-valent gold(III) complexes toward nucleophile-induced reductive elimination will lead to covalent protein modification by arylation. While most proteins are expressed amongst all cell types; protein overexpression is a common phenomenon in several cancer types due to their rapid proliferative phenotype and mutations compared to healthy non-cancerous cells. The nucleophilic amino acid side chains in proteins can be used as reactive handles for covalent modifications. Amongst the naturally occurring amino acids; cysteine, the most intrinsically nucleophilic, contains a highly reactive thiol functional group. This innate nucleophilicity provides a framework for covalent modification with electrophiles, which includes but is not limited to electron-deficient metal centers (e.g., Au and Pd).

Although there are previous reports successfully identifying transition metals as suitable chemical modifiers, specifically, tuning gold(III) complexes for selective binding offers a unique strategy for chemotherapeutics. Gold(III) metal centers are innately acidic and react with softer bases such as phosphorous and sulfur unlike the traditionally used late transition metals. Secondly, gold(III) complexes are known to target proteins over DNA, unlike other common transition metal complexes such as platinum and ruthenium. Combining the innate ability of gold(III) complexes to interact with proteins and the high affinity for cysteine thiols, rationale design of highly selective protein modifiers and efficient chemotherapeutics is possible.

My work focused on tuning the reactivity of cyclometalated gold(III) complexes for cysteine arylation and ligand-directed bioconjugation using Metal-mediated Ligand Affinity ��ɫ��Ƶ (MLAC) have been elucidated to modify biomolecules including antibodies and undruggable protein targets such as KRAS. While developing cyclometalated gold(III) complexes discussed herein, a unique class chiral gold(III) complexes bearing diamine or phosphine ligands led to other applications including improved anticancer activity in comparison to first generation of gold(III) complexes. A key highlight is the development of stable organometallic gold(III) macrocycles with potent in vitro and in vivo anticancer action in aggressive cancer types including triple negative breast cancer (TNBC).  

KEYWORDS: Site-selective protein modification, gold complexes, covalent binders, cysteine arylation, anticancer

Graduate Student Profile

Abstract: A thiol molecule, 2,6-pyridinediamidoethanethiol (PB9), was synthesized based on the pyridine-2,6-dicarboxamide scaffold with appended cysteamine group. PB9 acts as an effective chelator for Pb(II) due to multiple binding sites (N3S2) through irreversible binding precipitating Pb(II). Removal of aqueous Pb(II) from solution was demonstrated by exploring the effects of time, initial PB9:Pb(II) ratios, pH, exposure time, and solution temperature. After 15 min the Pb(II) concentrations were reduced from 50 ppm to 0.3 ppm (99.4%) and 0.25 ppm (99.5%) for PB9:Pb ratios of 1:1 and 2:1, respectively.  Removal of >93% Pb(II) was observed over multiple pH values with negligible susceptibility for leaching over time. The thermodynamic studies reveal the removal of Pb(II) from solution is an entropically driven spontaneous process. Solution-state studies (UV-Vis, 1H-NMR, 13C NMR) along with solid-state (IR, Raman, and thermal studies) for L/Pb(II) compounds were performed. UV-vis displays a global maximum at 274 nm and a local maximum at 327 nm for ligand-to-metal charge transfer S- 3p -> Pb2+ 6p, and intraatomic Pb2+ 6s2 -> Pb2+ 6p transitions.  A Probable molecular structure designed is PB9 behaving like a bis-deprotonated ligand with an N3S2 donor set to give Pb(II) a pentagonal environment with non-stereochemically active s electrons is proposed.  However, the existence of a cyclic oligomeric (PB9)4(Pb)4 or polymer (PB9)?(Pb)? structure is evident by broad melting point, insolubility in most common solvents, and amorphous powder XRD. PB9 also exhibits high sensitivity and selectivity towards Fe3+ over other metal ions, acts as a naked-eye detector showing colorless to yellow, and by fluorescent quenching. The quenching efficiency found by Stern-Volmer is 7.42 ± 0.03 × 103 M-1 with a higher apparent association constant of 9.537 X 103 M-1. A linear range of Fe3+ (0- 80 µM) with a detection limit of 0.59 µM (0.003 ppm) was found. The obtained detection limit was much lower than the maximum allowance limit of Fe3+ (0.3 ppm) regulated by EPA in drinking water.  Since Pb(II) removal using PB9 was higher than 15 ppb (EPA limit), a separate study was conducted to explore the use of thiol molecule (AB9) which was already developed in our lab previously. Thus, 2,2'-(isophthalolybis(azanaediyl))bis-3-mercaptopropanoic acid (AB9) was coupled to amine-functionalized silica and silica-coated magnetic nanoparticles (with Fe3O4 core). Results revealed successful fabrication of AB9 on mesoporous silica and MNPs surfaces without introducing crystalline impurities. Indeed, an added advantage for AB9-MNP over AB9-silica is its superparamagnetic nature where a magnet was used to isolate the Pb(II)-containing (solid) composite from the treated water. The >99.9% removal of Pb(II) was obtained by AB9-MNPs with detectable Pb(II) dropping to below 15 ppb EPA level. The obtained equilibrium results were in good agreement with the Langmuir model suggesting a dominant chemical adsorption mechanism on AB9- composites with monolayer coverage with maximum adsorption capacities of  24.80 and 56.40 mg/g respectively for AB9-silica and AB9-MNP implying the thiol group improved the adsorption capacity of Pb(II). This eco-friendly modification with rapid magnetic separation makes these AB9-MNPs a good candidate for aqueous Pb(II) removal

Abstract: To develop an effective battery cathode material that can be useful for future batteries, the thermal stability and ion migration dynamics need to be well understood. In situ transmission electron microscopy (TEM) is a popular and proven technique to study the evolution of local structures during the dynamic processes in the cathode materials. This dissertation will demonstrate the application of high-resolution imaging and in situ heating and biasing in the TEM to study the structure and composition, morphology change, and ion migration in the cathode materials.   The three chapters in this dissertation will be focused on the two cathode materials: zeta (?) vanadium pentoxide, and chromium intercalated sodium manganese oxide. The first project demonstrates the effect of in situ heating method, nanowire size, sodium content, and vacuum condition on the thermal stability of zeta (?) vanadium pentoxide in real-time in the TEM. The second project concentrates on in situ biasing in the TEM to study the sodium ion migration, silver exsolution, and negative differential resistance phenomenon in the zeta (?) vanadium pentoxide. The third project concentrates on the synthesis and characterization of chromium incorporated sodium manganese oxide. The works presented here show the capability of in situ TEM imaging techniques to study the dynamic changes in the structure and composition of the nanomaterials during the heating and biasing processes.

Jonathan Rivnay

Department of Biomedical Engineering and Simpson Querrey Institute

Northwestern University, Evanston, IL

Abstract: Direct measurement and stimulation of ionic, biomolecular, cellular, and tissue-scale activity is a staple of bioelectronic diagnosis and/or therapy. Such bi-directional interfacing can be enhanced by a unique set of properties imparted by organic electronic materials. These materials, based on conjugated polymers, can be adapted for use in biological settings and show significant molecular-level interaction with their local environment, readily swell, and provide soft, seamless mechanical matching with tissue. At the same time, their swelling and mixed conduction allows for enhanced ionic-electronic coupling for transduction of biosignals. Structure-transport properties allow us to better understand and design these active materials, providing further insight into the role of molecular design and processing on ionic and electronic transport, charging phenomena, and stability for the development of high-performance devices. Such properties stress the importance of bulk transport processes and serve to enable new capabilities in bioelectronics. In this talk I will discuss the design of new organic mixed conductors and future design rules for performance and stability. I will demonstrate how such materials properties relax design constraints and enable new device concepts and unique form factors, allowing for flexible amplification systems for electrophysiological recordings, and electroactive scaffolds to modulate tissue state and/or cell fate. New materials design continues to fill critical need gaps for challenging problems in bio-electronic interfacing.

Faculty Host: Dr. John Anthony

Speakers
	Dr. Erin Calipari Vanderbilt University Dr. Calipari received her PhD in Neuroscience in 2013 in the laboratory of Dr. Sara Jones at Wake Forest University School of Medicine where she studied how self-administered drugs altered dopaminergic function to drive addictive behaviors. She then went on to complete her postdoctoral training with Dr. Eric Nestler at Icahn School of Medicine at Mount Sinai, where she used circuit probing techniques to understand the temporally specific neural signals that underlie motivation and reward learning. She is currently an Assistant Professor at Vanderbilt University in the Department of Pharmacology. Her independent work seeks to characterize and modulate the precise circuits in the brain that underlie both adaptive and maladaptive processes in reward, motivation, and associative learning.
	Dr. Tim Harris Johns Hopkins University Timothy Harris is a research professor in the Department of Biomedical Engineering. He leads the Applied Physics and Instrumentation Group at the HHMI Janelia Research Campus, and is the originator of the project that produced the Neuropixels Si probe for extracellular recording in animals, mostly mice, and rats. He shares his time between Janelia and Johns Hopkins and is working on projects to enable recording 10-20,000 neurons in rodents and 30-50,000 neurons in non-human primates, as well as stimulate with high resolution. He received a BS in ��ɫ��Ƶ at California Polytechnical State University, San Luis Obispo, and a PhD in Analytical ��ɫ��Ƶ at Purdue University.
	Dr. Elizabeth Hillman Columbia University Elizabeth Hillman is professor of biomedical engineering and radiology at Columbia University and a member of the Mortimer B. Zuckerman Mind Brain Behavior Institute and Kavli Institute for Brain Science at Columbia. Hillman received her undergraduate degree in physics and Ph.D. in medical physics and bioengineering at University College London and completed post-doctoral training at Massachusetts General Hospital/Harvard Medical School. In 2006, Hillman moved to Columbia University, founding the Laboratory for Functional Optical Imaging. Hillman’s research program focuses on the development and application of optical imaging and microscopy technologies to capture functional dynamics in the living brain. Most recently, she developed swept confocally aligned planar excitation (SCAPE) microscopy, a technique capable of very high speed volumetric imaging of neural activity in behaving organisms such as adult and larval Drosophila, zebrafish, C. elegans and the rodent brain. Hillman’s research program also includes exploring the interrelation between neural activity and blood flow in the brain, as the basis for signals detected by functional magnetic resonance imaging (fMRI). Hillman is a fellow of the Optical Society of America (OSA), the society of photo-optical instrumentation (SPIE) and the American Institute for Medical and Biological Engineering (AIMBE). She has received the OSA Adolf Lomb Medal for contributions to optics, as well as early career awards from the Wallace Coulter Foundation, National Science Foundation and Human Frontier Science Program.
	Dr. Baljit Khakh University of California, Los Angeles Baljit Khakh completed his Ph.D. at the University of Cambridge in the laboratory of Patrick PA Humphrey. He completed postdoctoral fellowships in the laboratory of Graeme Henderson at the University of Bristol, and then in the laboratory of Henry A. Lester and Norman Davidson at California Institute of Technology. In 2001, Khakh became Group Leader at the MRC Laboratory of Molecular Biology in Cambridge, and in 2006 he moved to the University of California, Los Angeles where he is Professor of Physiology and Neurobiology. Khakh’s work has been recognized, including with the NIH Director's Pioneer Award, the Paul G. Allen Distinguished Investigator Award, and the Outstanding Investigator Award (R35) from NINDS.

2022 Naff Symposium Committee

- Chair